I can't think of any particular reason to wait for the upgrade. I believe you already need theme park reservations for the military MYW ticket so the argument that you'd need theme park reservations with an AP is a moot point. By upgrading earlier in your trip you can take advantage of any dining or shopping discounts (and if offsite the free parking). Either way, the AP will start with the first day you use the MYW ticket regardless of when you do the upgrade. Just don't wait until the day after you use the last entitlement on the MYW ticket. You can upgrade on the last day you use the ticket, but upgrade prior to park close that night.